1. ReDU: a framework to find and reanalyze public mass spectrometry data
- Author
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Universidad EAFIT. Departamento de Ciencias, Ciencias Biológicas y Bioprocesos (CIBIOP), Jarmusch A.K., Wang M., Aceves C.M., Advani R.S., Aguirre S., Aksenov A.A., Aleti G., Aron A.T., Bauermeister A., Bolleddu S., Bouslimani A., Caraballo Rodriguez A.M., Chaar R., Coras R., Elijah E.O., Ernst M., Gauglitz J.M., Gentry E.C., Husband M., Jarmusch S.A., Jones K.L., II, Kamenik Z., Le Gouellec A., Lu A., McCall L.-I., McPhail K.L., Meehan M.J., Melnik A.V., Menezes R.C., Montoya Giraldo Y.A., Nguyen N.H., Nothias L.F., Nothias-Esposito M., Panitchpakdi M., Petras D., Quinn R.A., Sikora N., van der Hooft J.J.J., Vargas F., Vrbanac A., Weldon K.C., Knight R., Bandeira N., Dorrestein P.C., Universidad EAFIT. Departamento de Ciencias, Ciencias Biológicas y Bioprocesos (CIBIOP), Jarmusch A.K., Wang M., Aceves C.M., Advani R.S., Aguirre S., Aksenov A.A., Aleti G., Aron A.T., Bauermeister A., Bolleddu S., Bouslimani A., Caraballo Rodriguez A.M., Chaar R., Coras R., Elijah E.O., Ernst M., Gauglitz J.M., Gentry E.C., Husband M., Jarmusch S.A., Jones K.L., II, Kamenik Z., Le Gouellec A., Lu A., McCall L.-I., McPhail K.L., Meehan M.J., Melnik A.V., Menezes R.C., Montoya Giraldo Y.A., Nguyen N.H., Nothias L.F., Nothias-Esposito M., Panitchpakdi M., Petras D., Quinn R.A., Sikora N., van der Hooft J.J.J., Vargas F., Vrbanac A., Weldon K.C., Knight R., Bandeira N., and Dorrestein P.C.
- Abstract
We present ReDU (https://redu.ucsd.edu/), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one’s own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.
- Published
- 2021